How to choose Home page version?

2. In the chosen Homepage editor locate the Override Global Settings – at the bottom of page editor:

3. All the settings (logo, alternate logo, colors, menu type, typography etc.) should be set the same in Customization panel.

Have a look at the following example - copying accent color (note: example is on the Craft Beer theme, but it works the same on all themes):

Once you are done with setting main settings in Customization panel (logo, accent and alternate colors, menu layout etc.) then make sure to edit Primary Menu according to your needs (remove unnecessary Homepages etc.).